>>>About seaview Program seaview was published in: Galtier, N., Gouy, M. & Gautier, C. (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 12:543-548. Binaries and full source code available from http://pbil.univ-lyon1.fr/software/seaview.html (C) 1996-2005 Manolo Gouy Laboratoire de Biometrie et Biologie Evolutive CNRS / Universite Lyon I Licensed under the GNU General Public Licence (http://www.gnu.org/licenses/gpl.txt) Seaview uses the FLTK project (http://www.fltk.org) for its user interface. Seaview uses the PDFlib Lite library (http://www.pdflib.com) for pdf output under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement. >>>Alignment panel Mouse Use: o Click on a site to position cursor (current cursor position -- sequence number, positions in alignment and in sequence -- appears at panel top center) o Click or drag mouse on several sequence names to group them (names will appear in black background). Alignment operations (gap insertions/deletions) will operate on all grouped sequences simultaneously. o Double-click on any name to group all sequences. #if WIN32 || __APPLE__ o Ctrl-Click somewhere in sequence names to move grouped sequences to another place in alignment. o Shift-Click to deactivate the current grouping; names return in normal print. #else o Click with middle mouse button somewhere in sequence names to move grouped sequences to another place in alignment. o Click with right mouse button to deactivate the current grouping; all names return in normal print. #endif Active keys: o The 4 keyboard arrows move the cursor o > < move the view by 50 sites to right and left (other keys can be used) o ] [ move the view by 5 sites to right and left (other keys can be used) see "Miscellaneous options" for how to use other keys for same purpose o - insert a gap in the cursor sequence and members of its group if any o or delete a gap at left of cursor o + inserts a gap in all sequences but that under the cursor and members of its group if any o _ ("underscore") deletes a gap in all sequences but that under the cursor and members of its group if any o 1234567890 (digit keys) allow to compose a number (appearing under mult=number at bottom left of panel) used as a multiplier to an operation to follow (e.g., keys 4, 5, and - in sequence will insert 45 gaps) o ctrl/cmd+S (according to platform) saves the alignment in the current filename using the current file saving format displayed by menu "Props". If format of the last loaded file does not match the current saving format, this key is not active. Mouse use on the site line (when there is one, white line at bottom): #if WIN32 || __APPLE__ o Click mouse to select/unselect a site. o Drag with the mouse button an extremity of a block of sites to extend or reduce it. o Ctrl-Click to extend the block of sites at left. o Shift-Click on a block of sites to delete it. #else o Click with the left mouse button to select/unselect a site. o Drag with the left mouse button an extremity of a block of sites to extend or reduce it. o Click with the middle mouse button to extend the block of sites at left. o Click with the right mouse button on a block of sites to delete it. #endif >>>File menu Open Mase, Open Phylip, Open Clustal, Open MSF, Open Fasta, Open NEXUS to load an alignment in one of these formats Mase and Nexus formats have the useful feature of allowing extra data beyond sequences and names (comments, accession numbers are really useful!). They can also store site sets [see item `Sites menu']. Save when active, saves the alignment in the current file (which name appears as window title). The shortcut for this operation is given. Save as... allows to save the alignment under a filename to be chosen in the file selector appearing next [Pressing button Rescan therein may be necessary to have all files appear]. Save current sites only active when a site line is displayed; allows to save in a file only those sites of the sequences where an X is in the site line. If some sequences are selected, only these are saved. #if __APPLE__ Prepare pdf Writes the alignment as a pdf file, with optional choices: #else Prepare pdf Writes the alignment as a pdf file. See options below. pdf options... allows to set several options for "Prepare pdf" menu item #endif fontsize sets the fontsize (font is Courier) block size alignment lines may be divided in blocks (e.g. of size 10 for DNA/RNA sequences or 3 for protein coding sequences) separated by one space to ease alignment reading. paper size: two paper formats can be used A4 or LETTER color/B&W choose between colored alignment or one with all black letters. variable sites only Available only in reference mode, allows to output only variable sites of the alignment and their positions. Quit guess what? >>>Props menu Fontsize > Tiny, Small, ..., Huge Sets the font size used to display sequences. Save format> Save as Mase, as Phylip, as Clustal, as MSF, as Fasta, as NEXUS Sets the file format used to save alignments [`Miscellaneous options' topic explains how to set default format] Colors > DNA/RNA colors Forces sequences to be colored as DNA/RNA in case they were erroneously recognized as protein data. > Protein colors Forces sequences to be colored as proteins in case they were erroneously recognized as DNA/RNA data. > Alt. colors Uses alternate coloring rules defined for protein sequences [`Coloring schemes' topic below explains how to define them]. > Inverted colors Display residues as black letters on colored background instead of as colored letters on grey background. Allow seq. edition When ON, residues can be deleted/inserted. when OFF (normally), only gaps can be deleted/inserted. by Reference To display the alignment by reference to a particular sequence: residues identical to that of the ref. seq. are displayed as dots. Possible only when one sequence, the reference, is selected and if not in inverted color mode. Alignment edition is impossible while in the reference mode. When used, File:Prepare pdf produces an output by reference. Combination ctrl/cmd+R is a shortcut for calling/exiting this mode. DNA keys Allows to use keys "hjkl" to enter DNA sequences "Allow seq. edition" should be ON for this item to be usable. Choose in the submenu what bases will be mapped to these keys > hjkl => GATC, hjkl => TCGA, hjkl => ACGT Also, the space bar will be mapped to base N. Clustalw options Allows to specify options sent to the clustalw alignment program in order to set, e.g., specific alignement parameter values. Go to submenu "Edit options" and type desired options in the dialog window that appears. #ifdef WIN32 An example is to type /gapopen=5 #else An example is to type -gapopen=5 #endif When an option has been typed it is active unless you switch it off by calling again "Clustalw options" and sliding to the check box. Thus a set of options can be memorized and turned on and off. Consensus option Allows to set the percent of identical residues needed to define a residue when building a consensus sequence. Sites where this fraction is not reached are filled with N or X. Fast-Rough Allows to switch between smooth-slow or rough-fast display. Allow lowercase If set, lowercase residues will be apparent. If not set, lowercase residues in sequence files display as uppercase. Customize To change, possibly permanently, various display settings. See "Miscellaneous options" and "Sequence coloring" help items. Apply: applies changes in current program session. Set changes permanent: applies changes in current and future program sessions. Close: ignores changes. >>>Sites menu Site sets allow to specify parts of a multiple alignment to be retained for further analyses (typically, those parts of the alignment taken as reliably aligned). Retained sites are depicted as series of Xs on a special line at bottom of the alignment panel. On color screens, they are also displayed by a dark background. Mouse clicks and drags on this line allow to construct/alter the set. Several sets of sites can be created and stored with the alignment if the Mase or NEXUS formats of alignment files are used. Each set has a name chosen by the user. One set of sites at most can be displayed at any time through this menu. Item "Save current sites" of menu "File" allows to save in an alignment file only those sites of the alignment pertaining to the currently displayed set. The resulting file may then be processed by, e.g., tree building programs. Create set creates a line at bottom of alignment to hold the location of alignment sites. Save set stores changes done to the current set of sites Rename set stores the current set of sites under a new name Hide set hides (but remembers except unsaved changes) the current set of sites Delete set removes the currently displayed set of sites from list of known sets shows a sites line of name constructed from data stored in the alignment, or previously created >>>Species menu Species sets can be created and stored with the alignment if the Mase or NEXUS formats of alignment files are used. To select one or several species, click or drag on their names; they will appear in black background. To memorize the current set of selected species, choose "Create set" from this menu. The program will ask for a name for this set. Delete set deletes (just from memory) the current set of species. Displays with black background the set of species memorized under that name. >>>Footers menu Comment lines can be created and displayed at bottom of the screen. These lines can contain any text and the program will maintain the vertical alignment between this text and sequences. This text can be saved using the mase or NEXUS file formats only. To edit this text, click on the line name, position the cursor, and type text. Click again on the line name to stop editing this text. Show / Hide footers To show / hide all footer lines Create footer To create a new footer line Delete footer To delete the currently selected footer line >>>Search button & box Type a string in box at right and strike key or push button to position the cursor in the next occurence of this string from its current place. Push button to position the cursor at next occurence of the current search string. Sequence gaps are ignored by the search procedure. >>>Goto button & box Moves the cursor to desired position or sequence Position: Type a number in box at right and hit key or push button to position the cursor at that position of the alignment. Sequence: Type a (fragment of) sequence name in box at right and hit key or push button to position the cursor in that sequence. Case is not significant. >>>Edit menu Rename sequence To rename the currently selected (= name in black background) sequence. Edit comments To see or change comments of the currently selected sequence (Comments can only be saved in mase/NEXUS). Delete sequence(s) Deletes all selected sequences from the alignment. Create sequence Allows to create a new-empty sequence in the alignment; set "Allow seq. edition" from "Props" menu ON to be able to type the sequence in. Load sequence Allows to load a new sequence in the alignment. The sequence can be typed in or pasted from a selection made in another window: drag on the sequence data, and paste it with the middle mouse button in the `Sequence loading' window. Duplicate sequence Allows to duplicate the currently selected sequence wih prefix D_ in its name. Complement sequence Creates a new sequence equal to the complementary strand of the currently selected sequence with prefix C_ in its name. Reverse sequence Creates a new sequence by reading 3' -> 5' the currently selected sequence and named with prefix R_ Exchange Us and Ts Exchange bases Us and Ts in all currently selected sequences. Align sites Runs the clustalw alignment program on the block of selected sites and the set of selected sequences. A window will ask for choosing the reference sequence: gaps present before clustalw alignment in the chosen sequence will be preserved in the new alignment. #ifdef WIN32 Program clustalw will be searched in the directory of the seaview program, the current directory and in directories of your PATH variable. #else Your PATH should contain the directories of programs clustalw, xterm and seaview_align.sh. #endif Dot plot Performs a "dot plot" analysis of the two selected sequences. See "Dot plot" item of the help data. Consensus sequence Computes the consensus of all currently selected sequences. At any site, the consensus residue is the most frequent one if its frequency is above a threshold value. This threshold (60 % by default) can be changed through item "Consensus threshold" of menu "Props". Below threshold, N or X is used. >>>Dot plot Performs a "dot plot" analysis of two sequences Enter desired values for the window size and # of matches/window, and click on button "Compute", the dot plot will appear. Click in the dot plot, the corresponding sequence regions appear in the alignment panel above the dot plot. Use "Magnify" to take a close look. Click on arrows at left to move the hit point by one residue in either of six directions. Move the slider below the alignment panel to control the number of displayed residues. Fit to window, Reduce, Magnify: perform zoom in and out operations Write Postcript: saves the dot plot in a file called from the alignment name with extension .ps Close: closes the dot plot window To perform a dot plot-guided alignment -------------------------------------- Click on a diagonal representing two sequence parts to be aligned, then click on button "align". Repeat this for each sequence parts you want to be aligned to each other. To transfer into the multiple alignment the result of these operations, click on button "Record alignment". Most often, one of the two compared sequences is already aligned to other sequences of the multiple alignment, while the other one is not. Choose which of the two sequences is already aligned by clicking on the arrow next to "Ref. sequence". >>>Mase file format Mase files follow the following format: Zero or more header lines each beginning with ;; Next, for each sequence in the alignment: One or more comment lines each beginning with ; Sequence name alone on a line (may be long and may contain spaces) Sequence data in free form, possibly with numbers and spaces ignored while reading the file. Dashes denote gaps. Header lines may contain any text and also contain descriptions of site sets and of species groups when such data have been defined. Site sets are written as in this example: ;;# of segments=10 mychoice ;; 14,74 221,256 416,449 990,1148 1363,1384 1474,1483 1556,1668 2034,2062 ;; 2114,2139 2756,2859 where "mychoice" is the name of the set of sites and where the series of pairs of numbers lists the endpoints of successive block of sites. Species groups are written as in this example: ;;@ of species = 4 distant outgroup ;; 2, 3, 4, 5 where "distant outgroup" is the name of the species group and where the series of numbers lists the ranks of sequences members of the species group. #if WIN32 || unix >>>Program arguments Program is run by command seaview [options] [filename] where options may be -save [format_name, either mase, clustal, phylip, msf, nexus or fasta sets the initial file format for saving operations and for opening the file given on command line; default is mase] -fast [sequences will be displayed faster but less smoothly] -inverted [residues will appear as black letters on a colored background] -fontsize n [sets to integer n the initial fontsize of the alignment panel] and filename is an optional alignment file to be loaded. The expected format for this file is that of the default format for saving operations. Use `Props:Customize' menu item to further customize the program. #endif >>>Sequence coloring The "Props:Customize" menu item allows to control colors. SETTING DNA/RNA SEQUENCE COLORING A,C,G,T/U buttons are colored using current color of the corresponding nucleotide. Click on a button to open a color chooser and select the desired color (OK will accept the new choice; reset will use the starting shade). "reset" will use default colors. "Apply" or "Set changes permanent" will apply new shades to current alignment. SETTING PROTEIN SEQUENCE COLORING aa coloring scheme: by default, amino acids are split in 8 families each displayed in a different color. These families can be customized, up to a maximum of 10. Also, an alternative coloring scheme can be defined, and seaview will allow to switch between the first and the alternative coloring schemes. catalog of amino acid colors: colors used for each amino acid family. Click on any to control the desired shade, as explained above. White is used for gaps and for unlisted residues. Example: with the default coloring scheme, groups of amino acids KR and AFILMVW are displayed with the first and second catalog colors, respectively. Click "reset" to use default amino acid families and color catalog. "Apply" or "Set changes permanent" to apply new shades to current alignment. >>>Miscellaneous options MISCELLANEOUS OPTIONS The "Props:Customize" menu item allows to set these options. [sites] background grey: move the slider to change the grey shade of the alignment panel background; the "sites" shade applies to selected sites only; "reset" gives default values to both shades. left-right movement keys: define 4 keys that move cursor right and left by 5 or 50 residues; reset uses default keys. pdf page format: sets the page format used by the "File:Prepare pdf" menu item. display lowercase: select so that lowercase characters present in sequence data are not displayed as uppercase. inverted: select to display sequences as black letters on colored background. default save format: sets the default format of the "File:save as" menu item. >>>Customization #ifdef __APPLE__ Custom settings are stored as program resources; so settings require write access to the seaview program to be permanently changed. #elif __WIN32__ Custom settings are stored in file seaview.ini in the same directory as seaview program. #else Custom settings are stored in file .seaviewrc in the user's home directory. #endif